population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data
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population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/03/30 13:48] – bngina | population-diversity:microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data [2020/04/29 10:14] – [Qiime2 data filtering and feature (OTU) table construction] bngina | ||
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- | #i create a directory to store all my '' | + | #i create a directory to store all my artifact i.e ' |
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+ | mkdir / | ||
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+ | #import the fastq files | ||
qiime tools import \ | qiime tools import \ | ||
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</ | </ | ||
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+ | We mentioned that qiime2 provides method to summarize and view artifacts by storing them as visualizations, | ||
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+ | < | ||
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+ | qiime demux summarize \ | ||
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+ | </ | ||
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+ | ==== Qiime2 data filtering and feature (OTU) table construction ==== | ||
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+ | Qiime2 provides two pluggins/ | ||
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+ | Important to keep in mind is the size of the amplified region covered by the primers used and what is the expected fragment length after read joining? This will determine the trim and truncate length parameters for dada2 and deblur pipelines. | ||
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+ | === Dada2 === | ||
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+ | The Dada2 pipeline detects and corrects illumina amplicon sequence data and additionally filter any phiX reads identified in sequencing data and also filter out any chimeric sequences. | ||
+ | To see usage and parameters that can be adjusted get the help for the pluggin i.e | ||
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population-diversity/microbiome-analysis-with-qiime2-using-illumina-paired-end-sequence-data.txt · Last modified: 2020/04/29 15:09 by bngina